3of 4Visiting from Minnetonka, Minn., Tom Clark and his mom, Carol Clark, get a picture with their catch.Photo: Liz Hafalia, The Chronicle

4of 4Chasin’ Crustacean docks at Fort Baker near Sausalito upon returning from a salmon fishing run.Photo: Liz Hafalia, The Chronicle

WASHINGTON — Water users in San Francisco and its suburbs face a day of reckoning as state regulators move to leave more water in California’s two biggest rivers in an effort to halt a collapse in the native ecosystem of the San Francisco Bay and its estuary, the Sacramento-San Joaquin River Delta.

Even as water allocations to California farmers have been severely reduced, San Francisco water authorities have freely tapped the Tuolumne River, which the city dammed early in the last century at its headwaters in Yosemite National Park.

Now the State Water Resources Control Board wants the city to help save the estuary by leaving 40 percent of the Tuolumne’s water in the river, a level that the board’s own scientists have said may not be enough to rescue the freshwater-starved bay and delta.

The Tuolumne is one of the most over-drafted rivers in the state, running on average at just 20 percent of its natural flow. The river provides 85 percent of the water used by 2.6 million Bay Area residents, including San Francisco.

Operator Christian Cavanaugh filets salmon for a passenger as Chasin'Crustacian returns to Fort Baker from a salmon fishing run on Friday, October 21, 2016, in Sausalito, Calif.

Photo: Liz Hafalia, The Chronicle

The draft rule, which the board hopes to make final next spring, could severely restrict water use during drought years, when there is not enough water for both the ecosystem and humans at current rates of consumption.

Jeffrey Mount, an expert in water policy at the Public Policy Institute of California, a nonprofit think tank, called the steps a long-overdue effort to “rebalance the allocation of water for the ecosystem and water we use consumptively.”

The Clean Water Act, a landmark federal environmental law, is driving a new approach, Mount said.

Mount, a senior fellow at the institute’s Water Policy Center, called the plan to leave more water in the rivers far weightier than the multibillion-dollar twin tunnels that Gov. Jerry Brown wants built to draw water directly from the Sacramento River, bypassing the delta, and send it to cities and farms in the south.

The controversial giant tunnels are “a sideshow” compared with the board’s attempt to guarantee a block of water to help the environment, Mount said.

Similarly, Spreck Rosekrans, head of Restore Hetch Hetchy, a group seeking to remove San Francisco’s dam in Yosemite, called the proposal to leave more water in the Tuolumne much bigger than the dam removal idea, which has been rejected by San Francisco voters.

“This is a big deal,” Rosekrans said of the draft rule, because it reduces the amount of water available for the city and its suburbs. Removing the Hetch Hetchy reservoir would still allow San Francisco to withdraw water from the river and store it elsewhere downstream.

State water board documents related to its proposal suggest that San Francisco might consider finding new sources of water through desalination or buying it from farmers.

State regulators said more water must be left in the Tuolumne and two other San Joaquin River tributaries, the Stanislaus and Merced, to halt an ecological crisis that threatens two salmon runs and several fish with extinction. Toxic algae blooms, rising prevalence of invasive species and other signs of failing ecological health abound in both the bay and the delta, they said.

California’s native salmon are a keystone species, providing food to plants and wildlife from the forests of the Sierra Nevada, where spawning fish leave their carcasses. Salmon are also the mainstay diet of the Orca whale, which feed on the fish at the mouth of San Francisco Bay.

On Wednesday, regulators took steps to leave more water in California’s largest river, the Sacramento, issuing a preliminary scientific report that analyzed the effects of letting anywhere from 35 to 75 percent of its waters flow to the ocean. Farms and cities use about half the river’s water, in effect reducing the amount that flows down the Sacramento.

The report and the San Joaquin draft rule together are meeting fierce opposition from northern San Joaquin Valley farmers and San Francisco water officials.

Michael Frantz, a board member of the Turlock Irrigation District and a wholesale nursery grower, confirmed reports that farmers across the northern San Joaquin Valley are in an uproar. He said the average farm in the Turlock district is just 26 acres, growing mainly permanent tree crops. Frantz said that had the draft rules been in place during the current drought, these farmers would have received no water for two years.

Bay Area water officials have joined the alarm, publishing an Oct. 7 opinion piece in The Chronicle that called the San Joaquin plan untenable, warning that it “means we would have to fundamentally rethink where we get our water in drought years and how we consume that water.”

The authors cited an earlier study by the San Francisco Public Utilities Commission that predicted that restrictions less harsh than what the draft rule calls for would result in water rationing and up to 188,000 in job losses along with nearly $50 billion in economic losses.

Peter Drekmeier, policy director for the Tuolumne River Trust, called the studyseriously flawed and accused the utilities commission of trying to scare people. He said if the projections were true, the Bay Area would have lost 24,510 jobs last year when the drought forced significant reductions in water use.

He said the state water board’s plan is “our last, best hope to revive the estuary.”

But Turlock’s Frantz urged the board to consider other methods to save the ecosystem, from building gravel beds for salmon to reducing invasive predator fish. He said Turlock farmers are prepared to “make a substantial financial contribution” to implementing such measures.

“Both San Francisco and the farming community have an intense desire to see the salmon fishery thrive, and we are convinced there are ways to get there without using so much water,” Frantz said.

State officials are welcoming such proposals but have made clear that water is what the ecosystem most needs. As it is, the board’s call for 40 percent of the San Joaquin’s natural flow to be left in the river, which could be adjusted up or down by 10 percent depending on wildlife needs, is far below the 60 percent flow that board scientists determined was needed.

John McManus, head of the Golden Gate Salmon Association, a fishing group, said Californians are simply facing the consequences of the fact that the state over the last century has promised people five times more water than nature provides.

“You can look in the rearview mirror of history and say we made some mistakes,” McManus said. State regulators, he said, now just happen to have “the unenviable task of being the last in line when the system breaks, and they have to right the wrongs.”

Carolyn Lochhead is the Washington correspondent for the San Francisco Chronicle, where she has covered national politics and policy for 22 years. She grew up in Paso Robles (San Luis Obispo County) and graduated from UC Berkeley cum laude in rhetoric and economics. She has a masters of journalism degree from Columbia University.